I was running PA 3.99, have made a backup using TWRP.
I have then wiped the phone, installed the new PA & GApp and rebooted. All is fine, I now have a clean fresh install of the latest PA.
Now what I wanted or at least thought was correct to do was restore using TWRP.... now this is my first mistake as all his does is restore it back to 3.99! DOH
So i then try again but with out wiping the system part. This time i keep 4+ but get stuck on a bootloader.

Basically all i am trying to do is restore my data IE all my exchange accounts and contacts etc which I thought would be done with the data part of TWRP.

All apps have re-installed with the help of google+ so is there a way to get the missing data back at all?

TWRP restores should not be done unless you want to restore the whole thing.

You have contradicting information, and clearly a lack of understanding the partition/folder structure layout of Android. The rom flash automatically WIPES system because /SYSTEM is where the ROM is stored. /DATA is where your data, apps, appdata, etc are stored. You should use Titanium Backup for backing up your apps/contacts (contacts should be synced with Google and not require backing up or restoring), call logs, mms/sms, etc.

I personally updated a galaxy nexus maguro, and 2 grouper (nexus 7 2012 wifi) from 3.99 to 4.0 with the OTA app, without wiping anything. From your 3.99 you should be able to do nothing more than install the new rom (gapps is even optional as the script keeps those installed anyway) and boot. dont wipe or restore anything. If that fails you should use the Titanium backup method instead.

Thanks. Yes I am still learning the whole process and obviously became confused. I will make sure from now on I use titanium backup properly. I thought team win was all I needed for backing up.
Thanks again.

For backing up app data, No. However in truth it is never a bad idea to keep a clean working backup image of an existing ROM in case all hell breaks loose on your device and need a copy of a previous image that you know works.

Needless to say it's preferable that you keep a copy this image some where other than on the storage partition of the device itself, like perhaps on your Google Drive space.

For backing up app data, No. However in truth it is never a bad idea to keep a clean working backup image of an existing ROM in case all hell breaks loose on your device and need a copy of a previous image that you know works.

Needless to say it's preferable that you keep a copy this image some where other than on the storage partition of the device itself, like perhaps on your Google Drive space.

XDA Developers was founded by developers, for developers. It is now a valuable resource for people who want to make the most of their mobile devices, from customizing the look and feel to adding new functionality.Are you a developer?